3TJI

CRYSTAL STRUCTURE OF AN ENOLASE FROM ENTEROBACTER sp. 638 (EFI TARGET EFI-501662) with BOUND MG

PDB DOI: https://doi.org/10.2210/pdb3TJI/pdb

Classification: LYASE
Organism(s): Enterobacter sp. 638
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-08-24 Released: 2011-09-14
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.282
R-Value Work: 0.252
R-Value Observed: 0.252

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of an enolase from enterobacter sp. 638 (efi target efi-501662) with boung mg

Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 190.67 kDa
Atom Count: 14,219
Modelled Residue Count: 1,596
Deposited Residue Count: 1,688
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein	A, B, C, D	422	Enterobacter sp. 638	Mutation(s): 0 Gene Names: Ent638_0932
UniProt
Find proteins for A4W7D6 (Enterobacter sp. (strain 638)) Explore A4W7D6 Go to UniProtKB: A4W7D6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4W7D6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	F [auth A], L [auth B], Q [auth C], W [auth D], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain W [auth D] Focus chain X [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D]	G [auth A] H [auth A] I [auth A] J [auth A] M [auth B] G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C], U [auth C], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain V [auth D]	E [auth A], K [auth B], P [auth C], V [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.282
R-Value Work: 0.252
R-Value Observed: 0.252
Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.15	α = 90
b = 182.15	β = 90
c = 104.8	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOSFLM	data reduction
PHASES	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-09-14

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2011-09-14
Type: Initial release
Version 1.1: 2012-02-22
Changes: Structure summary
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description